BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472402.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 20,344,376 number of mapped reads = 20,191,266 (99.25%) number of supplementary alignments = 77,654 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,122,247 number of mapped paired reads (second in pair) = 10,069,019 number of mapped paired reads (both in pair) = 20,098,592 number of mapped paired reads (singletons) = 92,674 number of mapped bases = 1,981,472,450 bp number of sequenced bases = 1,981,236,210 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,034,895 duplication rate = 48.18% >>>>>>> Insert size mean insert size = 16,249.3825 std insert size = 1,259,290.151 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 55.2543 >>>>>>> ACTG content number of A's = 536,293,373 bp (27.07%) number of C's = 455,138,113 bp (22.97%) number of T's = 536,670,722 bp (27.09%) number of G's = 452,878,391 bp (22.86%) number of N's = 255,611 bp (0.01%) GC percentage = 45.83% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 10,732,692 number of insertions = 122,457 mapped reads with insertion percentage = 0.6% number of deletions = 103,150 mapped reads with deletion percentage = 0.5% homopolymer indels = 45.3% >>>>>>> Coverage mean coverageData = 0.6401X std coverageData = 19.5748X There is a 5.33% of reference with a coverageData >= 1X There is a 2.31% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.33% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.31% of reference with a coverageData >= 18X There is a 0.3% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.29% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.28% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.27% of reference with a coverageData >= 25X There is a 0.27% of reference with a coverageData >= 26X There is a 0.26% of reference with a coverageData >= 27X There is a 0.26% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.25% of reference with a coverageData >= 30X There is a 0.25% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.23% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.22% of reference with a coverageData >= 40X There is a 0.22% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.21% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.21% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.2% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 202679063 0.8131536932058436 22.67745439949676 chr2 243199373 118695556 0.4880586431446104 14.631686855116063 chr3 198022430 172024375 0.8687115646444699 18.734213033996713 chr4 191154276 75400349 0.39444761884374485 14.461100316716678 chr5 180915260 112695278 0.6229174808139457 20.975676630247833 chr6 171115067 146248090 0.8546768707398513 23.24854314263586 chr7 159138663 111491131 0.7005911002281073 19.374733242166144 chr8 146364022 108852845 0.7437131305396896 19.801795769873657 chr9 141213431 97773910 0.692383927701608 17.30072603242235 chr10 135534747 37891632 0.27957134859299215 9.026168667245074 chr11 135006516 82075472 0.6079371161611192 16.878398896313367 chr12 133851895 115354638 0.8618080304354302 26.458431207383565 chr13 115169878 42497859 0.36900151096799805 13.311888936766554 chr14 107349540 57167648 0.5325374286652742 20.472089455707728 chr15 102531392 48426945 0.4723133477013557 15.663792872103313 chr16 90354753 86649603 0.9589933027651573 28.909255772661236 chr17 81195210 71332054 0.8785253957714994 22.358566862233065 chr18 78077248 34449429 0.4412223776124896 12.859810635545433 chr19 59128983 71790231 1.2141293044055907 35.47173403735774 chr20 63025520 46446493 0.7369473984506594 24.82010566378098 chr21 48129895 15739720 0.3270258536819995 18.394844642536803 chr22 51304566 32556380 0.6345708099353184 25.769204675645625 chrMT 16571 1136 0.06855349707320017 0.2856497037688322 chrX 155270560 89728319 0.577883656760174 15.58363794629685 chrY 59373566 3504294 0.059021113874143924 3.618089575560614